INTRODUCTION AND IMPORTANCE: Complete removal of the choledochal cysts (CC) with biliary enteric reconstruction is the standard treatment. The preferred biliary reconstruction, by either hepaticoduodenostomy (HD) or Roux-en-Y hepaticojejunostomy (RYHJ) remains a personal choice according to the surgeon's preference and experience. We report our long-term follow-up using an alternative method of biliary-enteric anastomosis without Roux-en-Y. CASE PRESENTATION: Two children (1½ and 4½ years old) with type I CC, diagnosed by CT scans or MRI in 2012 and 2013, underwent complete resection of the cysts and an end-to-side hepaticojejunostomy without Roux-en-Y (HJWRY) totally by laparoscopy. Bile leakage has occurred but, resolved spontaneously and oral feeding could be resumed. The children were discharged on the 6th and 8th postoperative days. At a 12-year follow-up, both children were doing well without complaints, and have shown no episodes of cholangitis. At the last follow-up, laboratory tests and ultrasound examinations were normal. CLINICAL DISCUSSION: The main treatment of choledochal cysts is their complete resection with biliary enteric reconstruction, which intends to mitigate the risk of malignancy and prevent postoperative cholangitis. The choice of enteric biliary reconstruction is still a matter of debate between HD and RYHJ, and this alternative HJWRY can be another strategy to compose the therapeutic options for the surgeon. CONCLUSION: Laparoscopic resection of choledochal cysts in children with the alternative HJWRY, appears to be a safe, simple, and reliable technique, does not facilitate reflux of bile into the stomach, has only one anastomosis, and could be considered a more physiological operation.